[BioC] ComBat

Peter Langfelder peter.langfelder at gmail.com
Mon Oct 28 18:46:30 CET 2013

ComBat says it found 5 batches instead of 4. That's your hint - it
seems your batch information is not read in correctly.


On Mon, Oct 28, 2013 at 9:22 AM, Kovyrshina, Tatiana
<tkovyrshina at houstonmethodist.org> wrote:
> Hello!
> I am trying to run ComBat on 4 batches of colorectal cancer that I got from the GEO website. I had success before with ComBat with different files, but for these R keeps giving me an error message:
>> ComBat("output_file.txt","Sample Information File.txt")
> Reading Sample Information File
> Reading Expression Data File
> Found 5 batches
> Found 1 covariate(s)
> Found 337 Missing Data Values
> Standardizing Data across genes
> Error in solve.default(t(des) %*% des) :
>   Lapack routine dgesv: system is exactly singular: U[1,1] = 0
> I tried running it only on the first 100 genes, same problem. I tried only the first 10 genes, same problem. I tried using only 2 batches and same problem. I ran SCAN, but I cannot attach the output file from that because it is too big. I did attach my sample information file.
> Do you have any suggestions for me about what could be wrong?
> Thank You!
> Tatiana Kovyrshina
> Houston Methodist. Leading Medicine.
> Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 13 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list eight years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.
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